New Mexico's spicy chiles can make grown men cry and ease the common cold, but they haven't fared well against root-rotting organisms known as Phytophthora.

Decades-long efforts by New Mexico State University researchers to grow a Phytophthora-fighting chile have proven largely futile. But scientists are now hoping that biotechnology and genetic research will help them create a new version lacking none of its ancestor's spice — and the state Legislature is providing some help.

Lawmakers recently approved a $250,000 annual appropriation to New Mexico State University for both genetic-engineering research and mechanical harvesting. Both are key to the industry's survival, say commercial chile growers.

"A lot of problems are solvable through conventional breeding," said Steve Hanson, assistant professor in NMSU's Department of Entomology, Plant Pathology and Weed Science. "Unfortunately, there are a couple of problems conventional breeding hasn't solved, like chile wilt."

But the idea of manipulating the genomic map of chile by inserting splices of DNA from other plants has traditional farmers and seed savers worried.

"Everyone in New Mexico wants the chile industry to be successful. We'd rather have it grown here than in China, and there's a lot of merit for the work NMSU is doing to help the chile industry be more competitive," said Paula Garcia, executive director of the New Mexico Acequia Association. But, she said, "When it comes to genetic engineering, they have to proceed with more safeguards and more consultation with stakeholders."

Garcia, who is also a member of the New Mexico Food and Seed Sovereignty Alliance, said the pueblos and small-scale farmers in the group oppose genetic engineering because of the potential for those seeds to cross with nongenetically modified seeds. She said state funding for genetic research conflicts with a memorial the Legislature approved last year protecting native seeds "from genetic contamination."

A stubborn problem

Phytophthora is the funguslike culprit in chile wilt, a disease the industry blames for repeatedly wiping out thousands of acres of the red and green fruits, and putting some commercial farmers out of business.

The organism was first described in New Mexico in 1922, but various strains of it date at least as far back as 1845, when it created havoc in Ireland by destroying potato crops.

Phytophthora usually attacks at the roots and lower stems of chile plants, causing the leaves to wilt. But in the last couple of decades, as irrigators sought ways to conserve water by using sprinklers, Phytophthora spread through the air to leaves, Hanson said, causing "a whole new problem by the same organism."

One of the reasons conventional breeding hasn't worked is that several different strains of Phytophthora are attacking the chiles. NMSU researcher Paul Bosland has successfully bred chile lines that are resistant to some strains but not others. Hanson said this is similar to the problem doctors are having now with the flu vaccine: It is effective against some but not all types of the flu virus. "New Mexico growers would be better off if they could battle only one type of Phytophthora," he said.

New tools

While Hanson's lab is looking at engineering chile genes to be more resistant to diseases and pests, no one there has so far developed any transgenic stock. "It is something we are working on. But we are not (conducting) any field trials. We don't know how to put genes into chiles right now," he said.

Meanwhile, the NMSU scientists are looking at other avenues for helping chile growers. One is a DNA-based test that would enable farmers to quickly identify the Phytophthora strain or other microorganisms killing chiles. Hanson likened it to a fingerprint test for plant pathogens, which would allow farmers to identify a potential chile-wilt problem within days instead of weeks. "Chile wilt, or blight, is public enemy number one for the chile growers," Hanson said. "The difficult thing about this disease is that several different organisms can cause the disease. It is important (for treatment) to know which one you are dealing with."

His lab successfully identified a bacterium as the source of a relatively new disease that causes chile plants to overgrow without producing fruit. The lab also developed a test to identify the microbe.

Another research project is looking at wild chile relatives or closely related plants, such as tomatoes and potatoes, that might have a natural resistance to chile wilt and other organisms deadly to chile. "We're looking to see if there are sources of resistant relatives that we might be able to use to make resistant chiles in the future," Hanson said.

Once his lab can find and map the genetic code for a Phytophthora-resistant chile cousin, there's a way to mark the resistant gene. Conventional breeders can then cross their chiles with the resistant cousin and track whether the offspring carry the marked gene for fighting Phytophthora.

"It's an area where biotechnologists like myself collaborate with conventional breeders," Hanson said.

His lab and other NMSU researchers also have projects under way to develop natural, biological controls for Phytophthora instead of using chemicals. "We've got a big project out here characterizing the natural microbial populations in healthy soil," Hanson said. "We're looking for beneficial organisms and actively screening for bacteria that might grow naturally on chile roots and prove antagonistic to Phytophthora."

Such a bacterial biocontrol could be used by chile growers the way organic farmers employ natural enzymes to improve the health of their soil.

Hanson said while he knows genetic engineering worries some people, he said the alternative for combating chile wilt and nematodes, or roundworms, is using chemical fungicides and pesticides. "There's lots of environmental damage associated with that," he said.

Methyl bromide, a soil fumigant, has proven one of the few pesticides effective against nematodes. But it sterilizes the soil, killing beneficial insects as well as nematodes.

And the U.S. Environmental Protection Agency is slowly instituting a ban against methyl bromide because of its impact on the ozone layer. That will leave farmers with few ways to combat nematodes.

"I see our genetic research on chile wilt and nematodes as having a big impact on sustainability and environmental protection," Hanson said. "If we can identify a couple of genes to make chile plants resistant, we can manage (the pests) while applying a lot less chemicals to fields."

Genetic-engineering concerns

The New Mexico Chile Association's Web site includes a long list of "best practices" for growing chile, learned through decades of trial, error and research. Growers rotate their crops and try to keep their soil healthy with fertilizers. Even so, chile wilt seems to get the upper hand. "This past year, one of the largest growing areas in (Southern) New Mexico was pretty much devastated because of widespread plant disease," said Gene Baca, president of the association. "Farmers, agronomists, plant breeders, chemical suppliers and everyone you can think of has been working on the Phytophthora problem for decades with little progress."

Genetic engineering might offer the answer, he said.

But Phil Loomis, an organic farmer in the Pojoaque Valley and president of the Santa Fe Farmers Market, said one problem might be large-scale commercial farming. He loses some of his chiles to wilt every year, he said. "But I think because of the organic techniques I use and the smaller scale and crop rotation, it is not such a problem for me. I think it is an issue for the big megafarms."

Baca and Hanson are well aware of other farmers' concerns over genetic engineering. Hanson said recent mistakes with field trials that have allowed genetically modified grass and canola to escape into the environment, for example, haven't helped the public's perception of genetic engineering. "Scientists all over the world realize the danger of releasing genes into the environment," Hanson said. "If you release the wrong one, it can create lots of problems."

Both say even if a genetically modified chile is developed years down the road, there are reliable ways to keep it from crossing with wild or traditional seed stock.

Baca notes some of those old lines have been protected already from crossing with hybrid chile seeds or other heritage seeds by separating or isolating crops. "We need to ensure the old lines are preserved for cultural and scientific reasons," Baca said. "The good news is these lines have been preserved from crossing with the hundreds of modern varieties now in use such as Sandia, Big Jim, NMex 6-4, Arizona 20 and all jalapeño, paprika and cayenne varieties. The same protections that people use now to keep their lines pure will continue to work in the future."

Hanson said modern agriculture developed important hybrid seeds for chiles and other crops, but overall seed diversity shrank as a result. He said NMSU researchers don't want that to continue. "The genetics and diversity are incredibly important," Hanson said.

Garcia said NMSU seems willing to work with the alliance and traditional farmers to keep them informed of where the research is headed. But she said they still believe the stakes are high and extra caution is vital.

"Things that were thought to be safe at one time, like asbestos and lead in gasoline, were later found to be unsafe," Garcia said. "But those were chemicals that could be called back, removed and contained. Genetic engineering is different. It is so long-term, so permanent."

With the issue of genetically modified corn and other seeds potentially impacting traditional, heritage seeds, the potential for the same thing to happen with chile is too serious to ignore, she said. "Many seeds are cultivated successfully for generations and shouldn't be threatened," she said. "I think these native seeds are our best hope for the future, for adapting to climate change and drought."

Contact Staci Matlock at 470-9843 or smatlock@sfnewmexican.com.